This proposal explores the basis for the different Rev/RRE activities that evolve in patients during infection, and also addresses how the structure of the RRE regulates Rev function. It also examines if the modulation of Rev/RRE function plays a role in two different clinical scenarios. Recent data, obtained by single genome sequencing, show that both Rev and RRE activity in an infected individual vary as HIV evolves, and that this variation arises from only a few changes in either Rev or RRE sequence. This change in Rev/RRE activity can profoundly affect rates of viral replication. The data also show that the pairing of any particular Rev sequence with different RREs leads to significant changes in overall Rev/RRE activity levels. This emphasizes the importance of analyzing Rev and RRE as a cognate pair derived from the same viral genome. At the present time, there is no mechanistic understanding of how small changes in sequence of either Rev or RRE modulate their combined activity. One of the aims of this proposal addresses this issue. We have also recently obtained data that demonstrate that the RRE is a dynamic RNA structure. In particular, stem loop regions III and IV can exist either as a single stem loop or as two separate ones, and the two structures probably are in equilibrium. Our data suggest that the formation of the structure with the individual stem loop IV is critical for Rev and RRE function. Another aim will examine the mechanistic basis for this. In the last aim, we will also further explore the hypothesis that good immune control selects for viruses with lower Rev/RRE activity. In addition we will also examine if viruses with lower Rev/RRE activity are favored in establishment of latently infected cells. The specific aims are: Specific Aim #1: What is the functional significance of the stem loop III/IV RRE sequence rearrangement? Specific Aim #2: What is the basis for the differences in activity that are observed with selected Rev- RRE pairs derived from infected patients? Specific Aim #3: Analysis of Rev-RRE activity in two different clinical scenarios.